Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

本研究旨在通过全基因组测序（Whole Genome Sequencing, WGS）技术鉴定基因组变异，并揭示与印度牦牛种群适应及生存适合度相关的生物学通路。本研究共纳入30份样本（每个种群10份），样本来源于阿鲁纳恰尔牦牛、喜马偕尔牦牛与拉达克牦牛三个种群。全基因组测序分析显示，阿鲁纳恰尔牦牛、喜马偕尔牦牛及拉达克牦牛中分别检出32171644、27260825、32632460个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），以及4865254、4429941、4847513个插入缺失变异（Insertions-Deletions, Indels）。RYR2、SYNE2、BOLA、HF1以及新转录本ENSBGRG00000011079等基因在三个牦牛种群中均携带最多的高影响变异，可能在当地适应性演化过程中发挥核心作用。对携带高影响单核苷酸多态性的基因开展功能富集分析后发现，其显著富集于应激响应、免疫系统调控以及高海拔适应相关通路。本研究全面解析了印度牦牛种群的基因组变异及其注释信息，可为牦牛相关研究人员提供宝贵的数据资源。此外，通过估算有效种群大小、近交系数、观测杂合度与期望杂合度等群体遗传学参数，本研究成果可用于优化牦牛保护策略。